def cbf_to_dat(lpin):
lpdir = os.path.dirname(lpin)
filename = None
params = {}
ofs_abs = open(os.path.join(lpdir, "corfac_absorp.dat"), "w")
ofs_abs.write("file ix xmin xmax ipos posx posy fac\n")
ofs_mod = open(os.path.join(lpdir, "corfac_modpix.dat"), "w")
ofs_mod.write("file ix xmin xmax iy ymin ymax fac\n")
ofs_dec = open(os.path.join(lpdir, "corfac_decay.dat"), "w")
ofs_dec.write("file ix xmin xmax iy ymin ymax fac\n")
for l in open(lpin):
if l.startswith(" CORRECTION FACTORS for visual inspection"):
filename = l.split()[-1]
elif l.startswith(" NUMBER OF REFLECTIONS USED FOR DETERMINING"):
nref = int(l.split()[-1]) # not used now
# open cbf
data, ndimfast, ndimmid = cbf.load_minicbf_as_numpy(os.path.join(lpdir, filename))
data = data.reshape(ndimmid, ndimfast)
filenum = filename[filename.index("_")+1:-4]
xmin, xmax = float(params["XMIN"][0]), float(params["XMAX"][0])
nxbin = int(params["NXBIN"][0])
xstep = (xmax-xmin)/nxbin
if "ABSORP_" in filename:
for ix in xrange(nxbin):
x1, x2 = xmin + ix*xstep, xmin + (ix+1)*xstep
for ipos in xrange(len(params["DETECTOR_SURFACE_POSITION"])):
pos = params["DETECTOR_SURFACE_POSITION"][ipos]
fac = data[ipos, ix]
ofs_abs.write("%s %2d %.2f %.2f %2d %s %5d\n" % (filenum, ix, x1, x2, ipos, pos, fac))
elif "DECAY_" in filename or "MODPIX_" in filename:
ymin, ymax = float(params["YMIN"][0]), float(params["YMAX"][0])
nybin = int(params["NYBIN"][0])
ystep = (ymax-ymin)/nybin
for ix in xrange(nxbin):
x1, x2 = xmin + ix*xstep, xmin + (ix+1)*xstep
for iy in xrange(nybin):
y1, y2 = ymin + iy*ystep, ymin + (iy+1)*ystep
fac = data[iy, ix]
ofs = ofs_mod if "MODPIX_" in filename else ofs_dec
ofs.write("%s %2d %.2f %.2f %2d %.5f %.5f %5d\n" % (filenum, ix, x1, x2, iy, y1, y2, fac))
else:
print "What is this file!?", filename
# reset
filename = None
params = {}
elif filename is not None:
r = xds.re_xds_kwd.findall(l)
for k, v in r:
params.setdefault(k, []).append(v)
def run(cbfin, cbfout, repl=None):
data, ndimfast, ndimmid = cbf.load_minicbf_as_numpy(cbfin)
max_I = max(data)
if repl is None:
repl = max_I+100
data[data<0] = repl
cbf.save_numpy_data_as_cbf(data, ndimfast, ndimmid, "negative_replaced", cbfout)
print "Launch:"
print "adxv -overload %d %s" % (max_I, cbfout)
def convert(cbfin, params):
if params.byteoffset:
import yamtbx_byteoffset_h5_ext
import pyublas
h5out = os.path.basename(cbfin) + ".h5"
data, ndimfast, ndimmid = cbf.load_minicbf_as_numpy(cbfin)
data = data.reshape((ndimmid, ndimfast))
if params.decompose:
data = decompose_panels(data)
header = XIO.Image(cbfin).header
of = h5py.File(h5out, "w")
grp = of.create_group("LCLS")
dset = grp.create_dataset("photon_energy_eV", (1, ), dtype=numpy.float)
dset[...] = 12398.4 / header["Wavelength"]
dset = grp.create_dataset("photon_wavelength_A", (1, ), dtype=numpy.float)
dset[...] = header["Wavelength"]
dset = grp.create_dataset("adu_per_eV", (1, ), dtype=numpy.float)
dset[...] = header["Wavelength"] / 12398.4
dset = grp.create_dataset("detector_distance_m", (1, ), dtype=numpy.float)
dset[...] = header["Distance"] / 1000.
dset = grp.create_dataset("beam_xy_px", (2, ), dtype=numpy.float)
dset[...] = (header["BeamX"] / header["PixelX"],
header["BeamY"] / header["PixelY"])
dset = grp.create_dataset("osc_step_deg", (1, ), dtype=numpy.float)
dset[...] = header["PhiWidth"]
cbfin = os.path.abspath(cbfin)
dset = grp.create_dataset("original_file", (1, ), "S%d" % len(cbfin))
dset[...] = cbfin
grp = of.create_group("data")
if params.byteoffset:
assert data.dtype == numpy.int32
# hid_t group_id, const std::string &name, const pyublas::numpy_vector<int> &data, int width, int height)
yamtbx_byteoffset_h5_ext.write_byteoffset_data(grp.id.id, "data",
data.ravel(),
data.shape[1],
data.shape[0])
else:
dset = grp.create_dataset("data", data.shape,
dtype=data.dtype) #, compression="CBF")
dset[...] = data
of.close()
print "Processed: %s" % os.path.basename(cbfin)
return data.shape
def run(cbfin, cbfout, repl=None):
data, ndimfast, ndimmid = cbf.load_minicbf_as_numpy(cbfin)
max_I = max(data)
if repl is None:
repl = max_I + 100
data[data < 0] = repl
cbf.save_numpy_data_as_cbf(data, ndimfast, ndimmid, "negative_replaced",
cbfout)
print "Launch:"
print "adxv -overload %d %s" % (max_I, cbfout)
def run(files, cbfout):
merged = None
for i, f in enumerate(files):
repl = -10 * (i+1)
print "%s %d" % (f, repl)
data, ndimfast, ndimmid = cbf.load_minicbf_as_numpy(f)
if i == 0:
merged = data.copy()
continue
merged[data==-10] = 65540 # repl # for adxv visualization. only assuming two files.
cbf.save_numpy_data_as_cbf(merged, ndimfast, ndimmid, "merged_predictions", cbfout)
def tst_h5toxds():
print "Testing H5ToXds.."
rcode, out, err = util.call("H5ToXds")
ignore_msg = "(You can ignore this if you don't process hdf5 files which usually mean Eiger data)"
if rcode == 127: # 127 is "command not found".
print " Not installed. NG %s" % ignore_msg
return False
import numpy
from yamtbx.dataproc.eiger import make_dummy_h5_for_test
from yamtbx.dataproc import cbf
tmpdir = util.get_temp_local_dir("h5test")
data = numpy.random.randint(0, 65535,
size=100).astype(numpy.uint32).reshape(
(1, 10, 10))
master_h5 = make_dummy_h5_for_test(tmpdir, data)
rcode, out, err = util.call("H5ToXds",
"%s 1 1.cbf" % os.path.basename(master_h5),
wdir=tmpdir)
cbfout = os.path.join(tmpdir, "1.cbf")
if not os.path.isfile(cbfout):
print " H5ToXds exists, but not works. Probably Dectris original H5ToXds? Test it with real h5 file. %s" % ignore_msg
if out.strip():
print " -- stdout:"
print out
if err.strip():
print " -- stderr:"
print err
shutil.rmtree(tmpdir)
return False
data_read, _, _ = cbf.load_minicbf_as_numpy(cbfout)
shutil.rmtree(tmpdir)
if numpy.all(data_read.flatten() == data.flatten()):
print " OK"
return True
else:
print " H5ToXds exists, but not correctly works. Probably Dectris original H5ToXds? Test it with real h5 file. %s" % ignore_msg
if out.strip():
print " -- stdout:"
print out
if err.strip():
print " -- stderr:"
print err
return False
def read_bkgpix_cbf(cbfin, positions):
data, nx, ny = cbf.load_minicbf_as_numpy(cbfin)
data = data.reshape(ny, nx)
npos = len(positions)
dists = numpy.array((data,)*npos)
gx, gy = numpy.meshgrid(xrange(nx), xrange(ny))
for i, pos in enumerate(positions):
print i, pos
dists[i,] = (gx-pos[0])**2 + (gy-pos[1])**2 # squared distance to each position
ret = dists.argmin(axis=0) + 1
ret[data < 0] = -10
return ret
def convert(cbfin, params):
if params.byteoffset:
import yamtbx_byteoffset_h5_ext
import pyublas
h5out = os.path.basename(cbfin) + ".h5"
data, ndimfast, ndimmid = cbf.load_minicbf_as_numpy(cbfin)
data = data.reshape((ndimmid, ndimfast))
if params.decompose:
data = decompose_panels(data)
header = XIO.Image(cbfin).header
of = h5py.File(h5out, "w")
grp = of.create_group("LCLS")
dset = grp.create_dataset("photon_energy_eV", (1,), dtype=numpy.float)
dset[...] = 12398.4/header["Wavelength"]
dset = grp.create_dataset("photon_wavelength_A", (1,), dtype=numpy.float)
dset[...] = header["Wavelength"]
dset = grp.create_dataset("adu_per_eV", (1,), dtype=numpy.float)
dset[...] = header["Wavelength"] / 12398.4
dset = grp.create_dataset("detector_distance_m", (1,), dtype=numpy.float)
dset[...] = header["Distance"]/1000.
dset = grp.create_dataset("beam_xy_px", (2,), dtype=numpy.float)
dset[...] = (header["BeamX"]/header["PixelX"], header["BeamY"]/header["PixelY"])
dset = grp.create_dataset("osc_step_deg", (1,), dtype=numpy.float)
dset[...] = header["PhiWidth"]
cbfin = os.path.abspath(cbfin)
dset = grp.create_dataset("original_file", (1,), "S%d"%len(cbfin))
dset[...] = cbfin
grp = of.create_group("data")
if params.byteoffset:
assert data.dtype == numpy.int32
# hid_t group_id, const std::string &name, const pyublas::numpy_vector<int> &data, int width, int height)
yamtbx_byteoffset_h5_ext.write_byteoffset_data(grp.id.id, "data", data.ravel(), data.shape[1], data.shape[0])
else:
dset = grp.create_dataset("data", data.shape, dtype=data.dtype)#, compression="CBF")
dset[...] = data
of.close()
print "Processed: %s" % os.path.basename(cbfin)
return data.shape
def run(files, cbfout):
merged = None
for i, f in enumerate(files):
repl = -10 * (i + 1)
print "%s %d" % (f, repl)
data, ndimfast, ndimmid = cbf.load_minicbf_as_numpy(f)
if i == 0:
merged = data.copy()
continue
merged[
data ==
-10] = 65540 # repl # for adxv visualization. only assuming two files.
cbf.save_numpy_data_as_cbf(merged, ndimfast, ndimmid, "merged_predictions",
cbfout)
def run(cbfin, binout):
# This function only returns signed int.
arr, ndimfast, ndimmid = cbf.load_minicbf_as_numpy(cbfin, quiet=False)
arr.tofile(binout)
print "Saved:", binout
print
print "Instruction for fit2d"
print " Width:", ndimfast
print " Height:", ndimmid
print " Type: Integer (%d byte)" % arr.dtype.itemsize
print " Signed: Yes"
print
print """Instruction for R
R
to.read<-file("%(filename)s","rb")
d <- readBin(to.read, integer(), size=%(size)d, signed=%(signed)s, n=%(width)d*%(height)d, endian = "little")
hist(d)
""" % dict(filename=binout, size=arr.dtype.itemsize, signed="TRUE", width=ndimfast, height=ndimmid)
def run(cbfin, binout):
# This function only returns signed int.
arr, ndimfast, ndimmid = cbf.load_minicbf_as_numpy(cbfin, quiet=False)
arr.tofile(binout)
print "Saved:", binout
print
print "Instruction for fit2d"
print " Width:", ndimfast
print " Height:", ndimmid
print " Type: Integer (%d byte)" % arr.dtype.itemsize
print " Signed: Yes"
print
print """Instruction for R
R
to.read<-file("%(filename)s","rb")
d <- readBin(to.read, integer(), size=%(size)d, signed=%(signed)s, n=%(width)d*%(height)d, endian = "little")
hist(d)
""" % dict(filename=binout,
size=arr.dtype.itemsize,
signed="TRUE",
width=ndimfast,
height=ndimmid)
def read_absorp_cbf(cbfin):
data, ndimfast, ndimmid = cbf.load_minicbf_as_numpy(cbfin)
data = data.reshape(ndimmid, ndimfast)
#fac = data[ipos, ix]
return data
def cbf_to_dat(lpin):
lpdir = os.path.dirname(lpin)
filename = None
params = {}
ofs_abs = open(os.path.join(lpdir, "corfac_absorp.dat"), "w")
ofs_abs.write("file ix xmin xmax ipos posx posy fac\n")
ofs_mod = open(os.path.join(lpdir, "corfac_modpix.dat"), "w")
ofs_mod.write("file ix xmin xmax iy ymin ymax fac\n")
ofs_dec = open(os.path.join(lpdir, "corfac_decay.dat"), "w")
ofs_dec.write("file ix xmin xmax iy ymin ymax fac\n")
for l in open(lpin):
if l.startswith(" CORRECTION FACTORS for visual inspection"):
filename = l.split()[-1]
elif l.startswith(" NUMBER OF REFLECTIONS USED FOR DETERMINING"):
nref = int(l.split()[-1]) # not used now
if "_***" in filename:
# reset
filename = None
params = {}
continue
# open cbf
data, ndimfast, ndimmid = cbf.load_minicbf_as_numpy(
os.path.join(lpdir, filename))
data = data.reshape(ndimmid, ndimfast)
filenum = filename[filename.index("_") + 1:-4]
xmin, xmax = float(params["XMIN"][0]), float(params["XMAX"][0])
nxbin = int(params["NXBIN"][0])
xstep = (xmax - xmin) / nxbin
if "ABSORP_" in filename:
for ix in xrange(nxbin):
x1, x2 = xmin + ix * xstep, xmin + (ix + 1) * xstep
for ipos in xrange(len(
params["DETECTOR_SURFACE_POSITION"])):
pos = params["DETECTOR_SURFACE_POSITION"][ipos]
fac = data[ipos, ix]
ofs_abs.write("%s %2d %.2f %.2f %2d %s %5d\n" %
(filenum, ix, x1, x2, ipos, pos, fac))
elif "DECAY_" in filename or "MODPIX_" in filename:
ymin, ymax = float(params["YMIN"][0]), float(params["YMAX"][0])
nybin = int(params["NYBIN"][0])
ystep = (ymax - ymin) / nybin
for ix in xrange(nxbin):
x1, x2 = xmin + ix * xstep, xmin + (ix + 1) * xstep
for iy in xrange(nybin):
y1, y2 = ymin + iy * ystep, ymin + (iy + 1) * ystep
fac = data[iy, ix]
ofs = ofs_mod if "MODPIX_" in filename else ofs_dec
ofs.write("%s %2d %.2f %.2f %2d %.5f %.5f %5d\n" %
(filenum, ix, x1, x2, iy, y1, y2, fac))
else:
print "What is this file!?", filename
# reset
filename = None
params = {}
elif filename is not None:
r = xds.re_xds_kwd.findall(l)
for k, v in r:
params.setdefault(k, []).append(v)
